Last time we saw how to extract the sequence from a GenBank file. This time we are going to parse some other information from these files. Basically we will use the same idea of our last post to extract the Organism name, the Locus and the Accession number of the item. From our last entry we have to remember this

sequence = ''
issequence = False
for line in gbfile:
    if issequence == True and not line.find('/') == 0:
        sequence += line.lstrip('0123456789 ').replace(' ', '')
    elif line.find('ORIGIN') >= 0:
        issequence = True

and modify it to our needs. Looks simple, and it is. Let’s see

import sys

gbfile = open(sys.argv[1], 'r').readlines()

locus = ''
organism = ''
accession = ''
for line in gbfile:
    if line.find('LOCUS') >= 0:
        locus = line
    elif line.find('ACCESSION') >= 0:
        accession = line
    elif line.find('ORGANISM') >= 0:
        organism = line

print locus.strip()
print organism.strip()
print accession.strip()

Just add a flag for each entry you want to parse and that’s it. For longer entries, such as the sequence, we have to use the same approach used before, with a boolean flag and concatenating the lines until another flag is found.

————-

Well, that’s it. After 46 entries we start a new phase. Still it will be beginning Python for bioinformatics.

1 gtttggtcct aaccttgtaa tcaattttta cttaatatac acatgcaagt ctccgcaccc
61 ctgtgaaaac gcccttaaat cccccatggg ataaggagct ggtatcaggc acgaaaatct
121 gcccaaaaca cctagctatg ccacacccac aagggtactc agcagtgatt gacattattt
181 ataagcgcca gcttgactca gttaaagtaa agagagccgg caaatctggt gccagccgcc
241 gcggttaccc cacgtggctc aaattgattt ctttcggcgt aaagcgtgat taaagtgccc
301 atcaacattg gagttaaact aaaattaagc tgtgacacgc ttattttaca gaaaagcaca
361 aacgaaagtt acttcaattt aaacaacttg aattcacgac agtcaggaca caaactggga
421 ttagataccc cactatgccc gaccgtaaac tttaatttac accatcaccg ccagagaact
481 acgagcaaag cttaaaactc aaaggacttg acggtccccc acatccccct agaggagcct
541 gtcctttaat cgataatccc cgcttaacct caccattctt agtctttcag cctgtatacc
601 tccgtcgtca gcttaccccg tgagcgaaaa ttagtgagct taatgtccac acgtctacac
661 gtcaggtcaa ggtgcagcaa atataatggg aagagatggg ctacactttc tagtctagaa
721 tatacgaaag accacctatg aaacctggtc agaaggcgga tttagaagta aaaggaaacc
781 agagcatccc ttttaatttg gcactggggc atgtacacac cgcccgtcac cctcttcaaa
841 gcctaatttt agtatctaac caactaacgc ctagtagaag aggcaagtcg taacatggta
901 agtataccgg aaggtgtgct tggaaacaaa atatagccta atcaaagcat ttcgcttaca
961 ccgaaaagtt atctgtgaaa ttcagattat tttgagctaa aaatctagcc ccactttatt
1021 ctataatccc ttatcactta aattcatgaa tcaaaacatt ttaataatca agtaaaggcg
1081 attgaaaaat taataggagc aatatatact gtaccgcaag ggaaagatga aatagaaatg
1141 aaataataat taaagcataa aaaagtaaag attaaatctt gtaccttttg catcatgatt
1201 taactagtct acccaggcaa aatgatttta agtctgacct cccgaaacta agtgagctac
1261 ttcaaggcag cttaatgagc aaatccgtct ctgtcgcaaa agagtggaga gaccttcaag
1321 tagaagtgat agacctaacg aacttagtaa tagctggtta ttcaagaaaa ggatctcagt
1381 ccaacctaaa gtcaaattaa tgtttaaaaa taaaaattct gaccttagag taattcaatt
1441 aaggtacagc ctacttgaaa caggatacaa ccttaactaa tgggtaactt accccttcat
1501 cttttaagtg ggcctaaaag cagccacctt taaaatagcg tcaaagctta gccgtcctat
1561 acatctaata ccaaaaacat ctatgaaccc tatactcata ttgaataatt ctatattatt
1621 atagagattt ttatgttaaa actagtaaca agaattaaat tttctctatt atgttcgtgt
1681 acatcagaaa ggataaacca ctgataattg acatgcatga gtaaaaagca gtaacttaac
1741 aagaaaaccc tcctaactct aatgttaacc taacacaagt acatctcaag aaagatttaa
1801 agaaaaagaa ggaactcggc aaacattaac ctcgcctgtt taccaaaaac atcgcctctt
1861 gtcaaaattt aagaggtcca gcctgcccag tgaccctgtt caacggccgc ggtatcctaa
1921 ccgtgcgaag gtagcgtaat cacttgttct ttaaataagg actagtatga atggcaccac
1981 gagggttata ctgtctcctt tttctaatca gtgaaactaa tcttcccgtg aagaagcggg
2041 aatttttata taagacgaga agaccctatg gagctttaga cgagtaacaa ctgctaattt
2101 tataatattt cagataatat ctctatccta gcattatgat tataagtctt tggttggggt
2161 gaccgcggag aaaaaaataa cctccacatt gaaagaatat tattctaagc aaaaagacac
2221 atctttaagc atcaacaaat tgacatctat tgacccaata ttttgatcaa cgaaccaagt
2281 taccctaggg ataacagcgc aatccacttc gagagctctt atcgacaagt gggcttacga
2341 cctcgatgtt ggatcagggt atcctagtgg tgtagccgct actaaaggtt cgtttgttca
2401 acgattaaaa ccct
//

Notice that there were no mention to the // at the end of the file This double slash represents the EOF of a GenBank file. Ideally we need to remove it from the final output, as we need to remove the nucleotide number at the beginning of each line. In order to do that we need to modify our last script.

First we will add a condition on the for loop that will take care of the double slash at the end. Then we need to use a trick to remove the numbers from the lines. We should expect the numbers to be at the beginning of the line, and never in another place. The long way would be to create a regular expression and then replace every number occurrence with an empty string. But Python comes with batteries included, so we will take the short path. We use the lstrip string method that will remove characters from the left part of the string, and set it to remove numbers from 0 to 9 and the extra space before the nucleotides. And our script will like this:

import sys

gbfile = open(sys.argv[1], 'r').readlines()

sequence = ''
issequence = False
for line in gbfile:
    if issequence == True and not line.find('/') == 0:
        sequence += line.lstrip('0123456789 ')
    elif line.find('ORIGIN') >= 0:
        issequence = True

print sequence

Notice that the first if condition was modified to include a condition that we do not find a slash. And at the line where we concatenate the sequence we added a lstrip('0123456789 ') to modify the string on the fly. The final result looks much better now. But we still have a small “problem”: there are spaces between groups of 10 nucleotides and we want to get rid of them. We would be surprised if it was difficult, and as expected it is not. We used here the replace method and we can use it here too. We only need to modify the line that concatenates the sequence, and our final script will be

import sys

gbfile = open(sys.argv[1], 'r').readlines()

sequence = ''
issequence = False
for line in gbfile:
    if issequence == True and not line.find('/') == 0:
        sequence += line.lstrip('0123456789 ').replace(' ', '')
    elif line.find('ORIGIN') >= 0:
        issequence = True

print sequence

Notice that we add the replace method after the lstrip, but it can either way. The output should be only the nucleotides, with no space or numbers.

The GenBank file we are going to manipulate from now on is this one

LOCUS DQ283072 2414 bp DNA linear VRT 23-MAR-2006
DEFINITION Megaelosia goeldii 12S ribosomal RNA gene, partial sequence;
tRNA-Val gene, complete sequence; and 16S ribosomal RNA gene,
partial sequence; mitochondrial.
ACCESSION DQ283072
VERSION DQ283072.1 GI:90296241
KEYWORDS .
SOURCE mitochondrion Megaelosia goeldii (Rio big-tooth frog)
ORGANISM Megaelosia goeldii
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Amphibia; Batrachia; Anura; Neobatrachia; Hyloidea;
Leptodactylidae; Cycloramphinae; Megaelosia.
REFERENCE 1 (bases 1 to 2414)
AUTHORS Frost,D.R., Grant,T., Faivovich,J., Bain,R., Haas,A.,
Haddad,C.F.B., de Sa,R.O., Channing,A., Wilkinson,M.,
Donnellan,S.C., Raxworthy,C., Campbell,J.A., Blotto,B.L., Moler,P.,
Drewes,R.C., Nussbaum,R.A., Lynch,J.D., Green,D.M. and Wheeler,W.C.
TITLE The Amphibian Tree of Life
JOURNAL Bull. Am. Mus. Nat. Hist. 297, 1-291 (2006)
REFERENCE 2 (bases 1 to 2414)
AUTHORS Frost,D.R., Grant,T., Faivovich,J., Bain,R., Haas,A.,
Haddad,C.F.B., de Sa,R.O., Channing,A., Wilkinson,M.,
Donnellan,S.C., Raxworthy,C., Campbell,J.A., Blotto,B.L., Moler,P.,
Drewes,R.C., Nussbaum,R.A., Lynch,J.D., Green,D.M. and Wheeler,W.C.
TITLE Direct Submission
JOURNAL Submitted (26-OCT-2005) Herpetology, Division of Vertebrate
Zoology, American Museum of Natural History, Central Park West at
79th Street, New York, NY 10024, USA
FEATURES Location/Qualifiers
source 1..2414
/organism=”Megaelosia goeldii”
/organelle=”mitochondrion”
/mol_type=”genomic DNA”
/specimen_voucher=”Paulo Nuin”
/db_xref=”taxon:209670″
/country=”Brazil: Rio de Janeiro, Teresopolis, Rio Beija
Flor, 910 m, 22′24′S, 42′69′W”
misc_RNA <1..>2414
/note=”contains 12S ribosomal RNA, tRNA-Val, and 16S
ribosomal RNA”
ORIGIN
1 gtttggtcct aaccttgtaa tcaattttta cttaatatac acatgcaagt ctccgcaccc
61 ctgtgaaaac gcccttaaat cccccatggg ataaggagct ggtatcaggc acgaaaatct
121 gcccaaaaca cctagctatg ccacacccac aagggtactc agcagtgatt gacattattt
181 ataagcgcca gcttgactca gttaaagtaa agagagccgg caaatctggt gccagccgcc
241 gcggttaccc cacgtggctc aaattgattt ctttcggcgt aaagcgtgat taaagtgccc
301 atcaacattg gagttaaact aaaattaagc tgtgacacgc ttattttaca gaaaagcaca
361 aacgaaagtt acttcaattt aaacaacttg aattcacgac agtcaggaca caaactggga
421 ttagataccc cactatgccc gaccgtaaac tttaatttac accatcaccg ccagagaact
481 acgagcaaag cttaaaactc aaaggacttg acggtccccc acatccccct agaggagcct
541 gtcctttaat cgataatccc cgcttaacct caccattctt agtctttcag cctgtatacc
601 tccgtcgtca gcttaccccg tgagcgaaaa ttagtgagct taatgtccac acgtctacac
661 gtcaggtcaa ggtgcagcaa atataatggg aagagatggg ctacactttc tagtctagaa
721 tatacgaaag accacctatg aaacctggtc agaaggcgga tttagaagta aaaggaaacc
781 agagcatccc ttttaatttg gcactggggc atgtacacac cgcccgtcac cctcttcaaa
841 gcctaatttt agtatctaac caactaacgc ctagtagaag aggcaagtcg taacatggta
901 agtataccgg aaggtgtgct tggaaacaaa atatagccta atcaaagcat ttcgcttaca
961 ccgaaaagtt atctgtgaaa ttcagattat tttgagctaa aaatctagcc ccactttatt
1021 ctataatccc ttatcactta aattcatgaa tcaaaacatt ttaataatca agtaaaggcg
1081 attgaaaaat taataggagc aatatatact gtaccgcaag ggaaagatga aatagaaatg
1141 aaataataat taaagcataa aaaagtaaag attaaatctt gtaccttttg catcatgatt
1201 taactagtct acccaggcaa aatgatttta agtctgacct cccgaaacta agtgagctac
1261 ttcaaggcag cttaatgagc aaatccgtct ctgtcgcaaa agagtggaga gaccttcaag
1321 tagaagtgat agacctaacg aacttagtaa tagctggtta ttcaagaaaa ggatctcagt
1381 ccaacctaaa gtcaaattaa tgtttaaaaa taaaaattct gaccttagag taattcaatt
1441 aaggtacagc ctacttgaaa caggatacaa ccttaactaa tgggtaactt accccttcat
1501 cttttaagtg ggcctaaaag cagccacctt taaaatagcg tcaaagctta gccgtcctat
1561 acatctaata ccaaaaacat ctatgaaccc tatactcata ttgaataatt ctatattatt
1621 atagagattt ttatgttaaa actagtaaca agaattaaat tttctctatt atgttcgtgt
1681 acatcagaaa ggataaacca ctgataattg acatgcatga gtaaaaagca gtaacttaac
1741 aagaaaaccc tcctaactct aatgttaacc taacacaagt acatctcaag aaagatttaa
1801 agaaaaagaa ggaactcggc aaacattaac ctcgcctgtt taccaaaaac atcgcctctt
1861 gtcaaaattt aagaggtcca gcctgcccag tgaccctgtt caacggccgc ggtatcctaa
1921 ccgtgcgaag gtagcgtaat cacttgttct ttaaataagg actagtatga atggcaccac
1981 gagggttata ctgtctcctt tttctaatca gtgaaactaa tcttcccgtg aagaagcggg
2041 aatttttata taagacgaga agaccctatg gagctttaga cgagtaacaa ctgctaattt
2101 tataatattt cagataatat ctctatccta gcattatgat tataagtctt tggttggggt
2161 gaccgcggag aaaaaaataa cctccacatt gaaagaatat tattctaagc aaaaagacac
2221 atctttaagc atcaacaaat tgacatctat tgacccaata ttttgatcaa cgaaccaagt
2281 taccctaggg ataacagcgc aatccacttc gagagctctt atcgacaagt gggcttacga
2341 cctcgatgtt ggatcagggt atcctagtgg tgtagccgct actaaaggtt cgtttgttca
2401 acgattaaaa ccct
//

which stores a sequence of a mitochondrial gene of a stream frog from South America, called Megaelosia goeldii, also known as Rio big-tooth frog. (get a better formatted file here)

Our fast task will be to extract the DNA sequence from the file. This sounds easy, and not surprisingly it is. If we take a closer look at the file we will see that the sequence starts after the mark ORIGIN. From what we have seen before we just need to read the file, the a boolean variable that checks for ORIGIN and concatenate everything after that. Something like this

import sys

gbfile = open(sys.argv[1], 'r').readlines()

sequence = ''
issequence = False
for line in gbfile:
    if issequence == True:
        sequence += line
    elif line.find('ORIGIN') >= 0:
        issequence = True

print sequence

Quick and easy. When we find ORIGIN, issequence has its state changed to True and the lines below will concatenated into a string. We print at the end.

Next time we will do more fancy things.