Mercurial > repos > abims-sbr > cds_search
diff scripts/S02_remove_too_short_bit_or_whole_sequence.py @ 1:c79bdda8abfb draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
author | abims-sbr |
---|---|
date | Thu, 09 Jun 2022 12:40:00 +0000 |
parents | eb95bf7f90ae |
children |
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--- a/scripts/S02_remove_too_short_bit_or_whole_sequence.py Fri Feb 01 10:26:37 2019 -0500 +++ b/scripts/S02_remove_too_short_bit_or_whole_sequence.py Thu Jun 09 12:40:00 2022 +0000 @@ -89,9 +89,9 @@ seq_nuc = dico_nuc[fasta_name] if "?" in seq: - seq = string.replace(seq, "?", "-") + seq = str.replace(seq, "?", "-") if "?" in seq_nuc: - seq_nuc = string.replace(seq_nuc, "?", "-") + seq_nuc = str.replace(seq_nuc, "?", "-") ## 4.1 ## [FILTER 1] : Detect and Replace short internal indel symbole (= "-" as for other longer gaps) by a "?" ## aa @@ -107,7 +107,7 @@ ## 4.2 ## [FILTER 2] : Remove short bits of sequence (<"MIN_LENGTH_BIT_OF_SEQUENCE_aa") LIST_sublist_aa=[] - S1 = string.split(seq, "-") + S1 = str.split(seq, "-") for element in S1: if len(element) > MIN_LENGTH_BIT_OF_SEQUENCE_aa: LIST_sublist_aa.append(element) @@ -126,7 +126,7 @@ for subsequence in LIST_sublist_aa: ## aa - START = string.find(seq, subsequence) + START = str.find(seq, subsequence) END = START + len(subsequence) seq_gap = seq_gap[:START] + seq[START:END] + seq_gap[END:] ## 4.4.2 ## and then replace the correponding gaps by coding subsequence in the sequence ## nuc @@ -135,11 +135,11 @@ seq_gap_nuc = seq_gap_nuc[:START_nuc] + seq_nuc[START_nuc:END_nuc] + seq_gap_nuc[END_nuc:] ## 4.5 ## Save new sequence in bash if not empty - seq_empty_test = string.replace(seq_gap, "-", "") + seq_empty_test = str.replace(seq_gap, "-", "") if seq_empty_test != "": new_bash_aa[fasta_name] = seq_gap - seq_empty_test = string.replace(seq_gap_nuc, "-", "") + seq_empty_test = str.replace(seq_gap_nuc, "-", "") if seq_empty_test != "": new_bash_nuc[fasta_name] = seq_gap_nuc @@ -180,8 +180,8 @@ ###Print if sys.argv[2] == "oui" : - print "\nIn locus with CDS considering Methionine : \n" + print("\nIn locus with CDS considering Methionine : \n") else : - print "\nIn locus with CDS regardless of the Methionine : \n" + print("\nIn locus with CDS regardless of the Methionine : \n") -print "\nTotal number of locus recorded = %d" %n0 \ No newline at end of file +print("\nTotal number of locus recorded = %d" %n0)