The script is used to summarize the base counts in fasta file. It outputs the number of A/T/C/G in each sequences in fasta file, and calculates the percentage of the four bases.
Download source file and compile, for example:
gcc FaATCG -o fatcg
./fatcg test.fasta# Calculating ATCG in test.fasta.
>ScTTTmV_1 A 6 0.206897
>ScTTTmV_1 T 5 0.172414
>ScTTTmV_1 C 12 0.413793
>ScTTTmV_1 G 6 0.206897
# Number of bases: 29
>ScTTTmV_2 A 5 0.227273
>ScTTTmV_2 T 3 0.136364
>ScTTTmV_2 C 3 0.136364
>ScTTTmV_2 G 11 0.500000
# Number of bases: 22
>ScTTTmV_3 A 7 0.184211
>ScTTTmV_3 T 7 0.184211
>ScTTTmV_3 C 6 0.157895
>ScTTTmV_3 G 18 0.473684
# Number of bases: 38
# --------- Summary -----------
# The number of sequences: 3
# The number of bases: 89
# Total number of A: 18 0.202247
# Total number of T: 15 0.168539
# Total number of C: 21 0.235955
# Total number of G: 35 0.393258
The output will be directed into stdin. The output contains the name of sequences in fasta file, base, count, and percentage.
# Number of bases: 29 is the total number of base, including N etc.
At the end of output, you can find a summary of the whole fasta file.
For further analysis, using grep to create a table which can be directly used in R/Python.
./fatcg test.fasta | grep "^>" > final.txt